Details
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Type:
Support
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Labels:None
Description
The Biostars post can be found here:
https://www.biostars.org/p/147826/
User kirannbishwa01 wrote Question: Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations:
I very much like the IGB tools and its features. While I have been able to make a good use of it, I have been facing a problem and can't seem to find a solution how much I try. I am trying to view the aligned tophat output (mapped.bam and junction files from aligned RNAseq data on the reference A. lyrata genome. When I load the lyrata genome on the IGB browser I can see the genome coordinate and the TAIRmRNA database (the annotated .gff file). But, after I upload a mapped.bam and junction file I am not able to see the alignment (aligned reads) with the reference and the annotation.
But, I figured that the mapped.bam and junction creates its own set of scaffold at the bottom of the default set of scaffold (one to one copy with default, but not sure why?). So, if I select a scaffold that the mapped.bam file has created I am able to see the mapped reads and the junctions but now cannot see the co-ordinate bases and the annotations. However, with A. thaliana genome there is no such problem with viewing the mapped output and junctions from RNAseq data along with genome coordinates and bases, TAIR10 mRNA database and several other databases from other labs.
Also, I see that updated version of phytozome data is available (V10.2). Is the data for A. lyrata available on IGB browser (V7) the same as V10.2?
Thanks,
Bishwa K.
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User Ann wrote Comment: Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations:
I also noticed that iPlant and Ensembl are using names 1, 2, 3, ... 9 instead of scaffold_1, scaffold_2, ... , scaffold_9, which are the names JGI and Phytozome appear to be using. These scaffolds (1 through 9) appear to correspond to the nine physical chromosomes of A. lyrata. I think it would be useful for IGB QuickLoad to syncrhonize with Ensembl and also iPlant, which gets its data from Ensemble. So I am also going to change the genome files in IGB QuickLoad to use names 1, 2, 3, etc instead of scaffold_1, scaffold_2, etc for the nine chromosomal sequences.
User kirannbishwa01 wrote Comment: Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations:
Hi Ann, Thanks a lot for fixing these issues. A. lyrata has 8 physical chromosomes. So, scaffold 1-8 should represent to Chr 1-8. While 9 & 10 should represent mitochondrial and chloroplast genomes. There are several other unmapped regions (should be all other scaffolds).
Thanks a lot again,
User Ann wrote Comment: Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations:
Quick followup: Looks like scaffold_9 is bigger than scaffold_10. Also, scaffold_9 has many gene annotations and scaffold_10 has none. The gene models on scaffold_9 look a lot like genes from nuclear chromosomes - they have introns, exons, splicing.
User Ann wrote Comment: Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations:
Another followup:
Code I used to change gene model names and scaffold names is (mostly) here:
User Ann wrote Comment: Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations:
The new files are now available on IGBQuickLoad. IGB is now using the longer, non-numeric names for gene models.
User Sam wrote Comment: Viewing the tophat output (mapped.bam and junctions) along with genome coordinates/bases and mRNA annotations:
If you perform the alignment yourself, it might be a good idea to actually load the fasta file together with the gtf file you used for alignment to try and visualize the mapping on the IGB. Most of the time, it might just be due to the naming problem. And just in case, you might want to read this if you want to know how to index your fasta file:
http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference